United again gave a game to Ipswich's Town's Ed Upson and two other trailists in Charlton Athletic defender Taylor Sinfield and Frenchman Manuel Sante.
Blues faced a strong Orient line-up but had an experienced forward line themselves in Scannell, Barnard and Laurent.
And it was the French forward, who has only just returned from a fractured ankle, who hobbled off after 52 minutes. But Blues Ricky Duncan is hopeful that Laurent's latest injury is not too serious.
Speaking to the Echo Ricky said: "There wasn't too much swelling and he iced it up right away. Francis was going to come off anyway because it was his first game back and hopefully the injury isn't too serious. We will find out more in the next couple of days."
About the game he continued: "We did OK and had a great chance to take the lead through Rhys but unfortunately he didn't take it. At times the players needed to be a little bit stronger but they are young and they will learn. They certainly have enough games coming up to do that in as well."
Laurent was replaced in attack by Rhys Henry and the youngster had a great chance to open the scoring in the 59th minute. However, after latching onto a through ball from Jamie Forshaw, Henry could only fire against the right post.
The miss proved costly as Orient opened the scoring 10 minutes later as Harry Baker blasted the ball home from 20 yards.
Orient sealed the game with a second two minutes from the end through a smart finish by Ryan Jarvis. Fit-again forward Lee Barnard played 62 minutes as he strives to improve his match fitness after a recent hamstring injury.
The Good Lord Lee Barnard played for just over an hour without any reaction to his recent hamstring injury and along with his brief subs appearance towards the end of the Crewe game will be hoping he has convinced Tilly of his fitness and a starting position against the Farmers.
Ex-Blue striker Wayne Gray returned for Orient and played the first 45 minutes, his first competitive game since suffering a ruptured cruciate ligament last August.
Southend United: Joyce, Kante, Jones, Sinfield (Harvey 76), Herd, Scannell, Upson, O'Keefe, Forshaw, Laurent (Henry 52), Barnard (Calver 62)
Unused Subs: Abbey, McDonald.